Re: Memory corruption error in SNESSolve

Here's the function.

PetscErrorCode FormFunction(SNES snes,Vec x,Vec f,void *ctx)
{
PetscScalar *xx,*ff,d;
PetscErrorCode ierr;
PetscInt i,n;

PetscFunctionBegin;
ierr = VecGetArray(x,&xx);CHKERRQ(ierr);
ierr = VecGetArray(f,&ff);CHKERRQ(ierr);
ierr = VecGetSize(x,&n);CHKERRQ(ierr);

double h = 1.0/(n-1) ;
d = (PetscReal)(n - 1); d = d*d;
double pos ;

ff[0] = xx[0]; // left boundary with Dirichlet = 0
// residual : (un-1 -2*un + un+1)/h^2 + Reaction*u - f
for (i=1; i<n-1; i++) {
pos = i*h ;
ff[i] = -Diffusion(pos, 0, 0, 0, xx[i])*d*(xx[i-1] - 2.0*xx[i] +
xx[i+1]) + Reaction(pos, 0, 0, 0, xx[i])*xx[i] - RHS(pos, 0, 0, 0,
xx[i]) ;
}
ff[n-1] = xx[n-1] - 1.0; // right boundary with Dirichlet = 1

ierr = VecRestoreArray(x,&xx);CHKERRQ(ierr);
ierr = VecRestoreArray(f,&ff);CHKERRQ(ierr);
PetscFunctionReturn(0);
}

One question though. If i use GetArray and RestoreArray to change the
values directly in memory, do i still have to make the
VecAssemblyBegin-End calls ?

Thanks again for the help Matt.

Vijay

On Jan 22, 2008 5:02 PM, Matthew Knepley <knepley@xxxxxxxxx> wrote:
> On Jan 22, 2008 3:54 PM, Vijay M < vijay.m@xxxxxxxxx> wrote:
> > Hi all,
> >
> > I am currently trying to use LibMesh with PETSc SNES solver to solve a
> > nonlinear Diffusion-reaction problem. The code works fine with 1
> > processor but when i use 2 processors for the exact same problem, it
> > throws me this error regarding memory corruption. I am not sure what
> > this error is about and was wondering if someone can help me out on
> > this. Note: My residual function is being called successfully and
> > returns the residual back without any problem since i can see some
> > print message at the end of the call ! Hence, this problem is not in
> > my custom FormFunction.
>
> Actually, it is very likely that the problem is in your FormFunction. The
> error is being reported because after every call to FormFunction, we
> walk the PETSc heap and validate all the pieces of memory we allocated.
> Something wrote over a piece of memory we already own, so the OS
> did not complain and you saw your printout, however there is still corruption.
> I would advise you to run 'valgrind' on the code. It is the best tool I have
> used for finding these kind of errors.
>
> Matt
>
>
> > [1]PETSC ERROR: PetscMallocValidate: error detected at
> > SNESComputeFunction() line 950 in src/snes/interface/snes.c
> > [1]PETSC ERROR: Memory at address 0xa5cf40 is corrupted
> > [1]PETSC ERROR: Probably write past beginning or end of array
> > [1]PETSC ERROR: Last intact block allocated in PetscStrallocpy() line
> > 82 in src/sys/utils/str.c
> > [0]PETSC ERROR: PetscMallocValidate: error detected at
> > SNESComputeFunction() line 950 in src/snes/interface/snes.c
> > [0]PETSC ERROR: Memory at address 0xa5cf30 is corrupted
> > [0]PETSC ERROR: Probably write past beginning or end of array
> > [0]PETSC ERROR: Last intact block allocated in PetscStrallocpy() line
> > 82 in src/sys/utils/str.c
> > [0]PETSC ERROR: --------------------- Error Message
> > ------------------------------------
> > [0]PETSC ERROR: Memory corruption!
> > [0]PETSC ERROR: !
> > [0]PETSC ERROR:
> > ------------------------------------------------------------------------
> > [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 7, Fri Oct 26
> > 14:21:35 CDT 2007 HG revision:
> > 2e223033ba960114833e1f9713ab393ec78c056f
> > [0]PETSC ERROR: See docs/changes/index.html for recent updates.
> > [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> > [0]PETSC ERROR: See docs/index.html for manual pages.
> > [0]PETSC ERROR:
> > ------------------------------------------------------------------------
> > [0]PETSC ERROR: ./myProg-opt on a linux-gnu named [1]PETSC ERROR:
> > --------------------- Error Message
> > ------------------------------------
> > [1]PETSC ERROR: Memory corruption!
> > [1]PETSC ERROR: !
> > [1]PETSC ERROR:
> > ------------------------------------------------------------------------
> > [1]PETSC ERROR: Petsc Release Version 2.3.3, Patch 7, Fri Oct 26
> > 14:21:35 CDT 2007 HG revision:
> > 2e223033ba960114833e1f9713ab393ec78c056f
> > [1]PETSC ERROR: See docs/changes/index.html for recent updates.
> > [1]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> > [1]PETSC ERROR: See docs/index.html for manual pages.
> > [1]PETSC ERROR: ----------------------------[cli_0]: aborting job:
> > application called MPI_Abort(comm=0x84000000, 78) - process 0
> > [cli_1]: aborting job:
> > application called MPI_Abort(comm=0x84000000, 78) - process 1
> > grove.ne.tamu.edu by vijaysm Tue Jan 22 15:47:58 2008
> > [0]PETSC ERROR: Libraries linked from
> > /state/partition1/local/petsc-2.3.3-p7/lib/linux-gnu-c-debug
> > [0]PETSC ERROR: Configure run at Fri Nov 9 15:02:46 2007
> > [0]PETSC ERROR: Configure options --with-cc=gcc --with-fc=ifort
> > --with-cxx=g++ --download-f-blas-lapack=1 --download-mpich=1
> > --with-shared=1
> > [0]PETSC ERROR:
> > ------------------------------------------------------------------------
> > [0]PETSC ERROR: PetscMallocValidate() line 139 in src/sys/memory/mtr.c
> > [0]PETSC ERROR: SNESComputeFunction() line 950 in src/snes/interface/snes.c
> > [0]PETSC ERROR: SNESSolve_LS() line 158 in src/snes/impls/ls/ls.c
> > [0]PETSC ERROR: SNESSolve() line 1871 in src/snes/interface/snes.c
> > [0]PETSC ERROR: main() line 395 in unknowndirectory/myProg.C
> >
> > If you need some more information, feel free to let me know. Thanks in advance !
> >
> > Vijay
> >
> >
>
>
>
> --
> What most experimenters take for granted before they begin their
> experiments is infinitely more interesting than any results to which
> their experiments lead.
> -- Norbert Wiener
>
>